Australia's defence chief says a former Indonesian general who was invited to give evidence at the Balibo inquest during a visit to Sydney last month was not involved in the 1975 killing of five Australia-based journalists in East Timor.

Air Chief Marshal Angus Houston says Jakarta Governor Sutiyoso, who served in East Timor at the start of the Indonesian occupation of the territory in 1975, told him he and his troops were not in the district where the reporters were killed.

"He was nowhere near Balibo at the time of that unfortunate incident. Indeed he was with another team in another town in East Timor," Air Chief Marshal Houston told reporters after meeting Governor Sutiyoso in the Indonesian capital of Jakarta. "I accept his explanation and I have never doubted his innocence," he said.

Mr Sutiyoso said last month two New South Wales police officers had barged into his hotel room in Sydney during an official visit and asked him to sign an invitation to testify in an inquest into one of the men who died, Brian Peters.

Indonesia lodged a formal diplomatic protest but the row was defused after the Australian ambassador in Jakarta and the New South Wales Premier Morris Iemma apologised.

Air Chief Marshal Houston says he expressed regret to Mr Sutiyoso for "the unacceptable circumstances". "The Governor is a long-standing friend of Australia. Those circumstances will never happen again," said the ADF chief, who was Mr Sutiyoso's classmate at an Australian military staff college in 1990.

In final submissions to the inquest last month, Mark Tedeschi, the counsel assisting the coroner, said the journalists were killed in Balibo to stop them reporting news of Indonesian military actions.

Official Indonesian reports have blamed the deaths on October 16, 1975, on crossfire as Indonesian forces entered East Timor in an incursion ahead of a full-scale invasion of the territory in December of the same year.

Air Chief Marshal Houston is in Indonesia to meet armed forces chief Joko Suyanto and Defence Minister Juwono Sudarsono. He says he met Mr Sutiyoso as an "old friend" who beat him at a tennis competition in Australia.